Handel Research Group
Modeling and Analysis of Infectious Diseases
at the individual and population level

General research tools

This section is mainly intended for potential group members so they know what they might be getting themselves into. If others profit from some of the information, even better.

Computation/Simulation software

Our current programming environment of choice is the free and Open Source software R. We use it for almost all of our projects. An R tutorial can be found on our teaching resources page. While not required, using R through R Studio makes working in R more user/beginner friendly. R Studio is also free.

Some of our research involves spatially explicit, agent based simulations. We currently write those simulations in NetLogo, a free agent based simulation platform. Netlogo is very easy to program, and quite powerful and flexible. Speed is not great, but decent.

Sometimes we need to do a bit of analytics. While Mathematica and Maple are the two main programs for analytical calculations, they are expensive. We have found that for our purpose, the freely available Maxima suffices.

Writing/Presentation software

If you need to write articles with equations, properly embedded figures and tables, etc., word processors such as MS Word are not too great. Use LaTeX instead. It usually comes pre-installed with most Linux distributions, a very good Windows implementation also exists. LaTeX needs getting used to. Instead of writing in a visual style, you write commands that tell the program what to do. But once you figured it out, it’s easy and fast.

You will also want a good reference manager. LaTeX uses BibTeX. A bibtex file is basically one long text file that contains all your references. A number of programs allow you to easily manage that file. A good open-source/cross-platform reference manager is JabRef. It has a nice GUI, can automatically import references from places such as PubMed, you can do fulltext search, etc. It runs on any machine that has Java installed. We also use Zotero and Mendeley, both of which have functionality beyond that provided by JabRef.

Another good way of writing quick reports is using Markdown. It’s nicely integrated with R through R Studio’s R Markdown extension. One can quickly produce good looking results. The nice thing is that one can convert it through pandoc into many useful formats, such as HTML, LaTeX or Word. Check out R Studio’s R Markdown introduction to learn more.

Other useful tools

Sometimes you don’t want big brother and others to see your data. That applies to personal data, as well as potentially sensitive public health data. You can use GnuPG to encrypt files/emails and VeraCrypt for things like flashdrives or hard disk partitions. To securely transfer files between computers over the internet, use ssh/scp. It’s pre-installed on Linux, WinSCP is good for Windows machines.

If you need to regularly synchronzie files between different machines, Dropbox, Google Drive or similar services are very useful. Dropbox even works nicely with large files, such as encrypted VeraCrypt containers.

If you can get people to send you their data, great! But often, that fails, even if the data is already published. A great tool to extract data from figures is the free program Engauge Digitizer. The program Data Thief provides similar functionality.